A C++ version of the %in% operator in R

问题

Is there any function in C++ equivalent to %in% operator in R? Consider the command below in R:

which(y %in% x)

I tried to find something equivalent in C++ (specifically in Armadillo) and I couldn't find anything. I then wrote my own function which is very slow compared to the R command above.

Here is what I wrote:

#include <RcppArmadillo.h>
// [[Rcpp::depends("RcppArmadillo")]]

// [[Rcpp::export]]
arma::uvec myInOperator(arma::vec myBigVec, arma::vec mySmallVec ){
 arma::uvec rslt = find(myBigVec == mySmallVec[0]);
 for (int i = 1; i < mySmallVec.size(); i++){
   arma::uvec rslt_tmp = find(myBigVec == mySmallVec[i]);
   rslt = arma::unique(join_cols( rslt, rslt_tmp ));
 }
 return rslt;
}

Now after sourcing in the code above, we have:

x <- 1:4
y <- 1:10
res <- benchmark(myInOperator(y, x), which(y %in% x), columns = c("test",
      "replications", "elapsed", "relative", "user.self", "sys.self"), 
       order = "relative")

And here are the results:

                 test replications elapsed relative user.self sys.self
 2    which(y %in% x)          100   0.001        1     0.001        0
 1 myInOperator(y, x)          100   0.002        2     0.001        0

Could anyone guide me either on finding a C++ code corresponding to which(y %in% x) or on making my code more efficient? The elapsed time is already very small for both functions. I guess what I meant by efficiency is more from programming perspective and on whether the way I thought about the problem and the commands I used are efficient.

I appreciate your help.

回答1:

EDIT: Thanks to @MatthewLundberg and @Yakk for catching my silly errors.

If what you really want is just faster matching, you should check out Simon Urbanek's fastmatch package. However, Rcpp does in fact have a sugar in function which can be used here. in uses some of the ideas from the fastmatch package and incorporates them into Rcpp. I also compare @hadley's solution here.

// [[Rcpp::plugins("cpp11")]]
#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
std::vector<int> sugar_in(IntegerVector x, IntegerVector y) {
  LogicalVector ind = in(x, y);
  int n = ind.size();
  std::vector<int> output;
  output.reserve(n);
  for (int i=0; i < n; ++i) {
    if (ind[i]) output.push_back(i+1);
  }
  return output;
}

// [[Rcpp::export]]
std::vector<int> which_in(IntegerVector x, IntegerVector y) {
  int nx = x.size();
  std::unordered_set<int> z(y.begin(), y.end());
  std::vector<int> output;
  output.reserve(nx);
  for (int i=0; i < nx; ++i) {
    if (z.find( x[i] ) != z.end() ) {
      output.push_back(i+1);
    }
  }
  return output;
}


// [[Rcpp::export]]
std::vector<int> which_in2(IntegerVector x, IntegerVector y) {
  std::vector<int> y_sort(y.size());
  std::partial_sort_copy (y.begin(), y.end(), y_sort.begin(), y_sort.end());

  int nx = x.size();
  std::vector<int> out;

  for (int i = 0; i < nx; ++i) {
    std::vector<int>::iterator found =
      lower_bound(y_sort.begin(), y_sort.end(), x[i]);
    if (found != y_sort.end()) {
      out.push_back(i + 1);
    }
  }
  return out;
}

/*** R
set.seed(123)
library(microbenchmark)
x <- sample(1:100)
y <- sample(1:10000, 1000)
identical( sugar_in(y, x), which(y %in% x) )
identical( which_in(y, x), which(y %in% x) )
identical( which_in2(y, x), which(y %in% x) )
microbenchmark(
  sugar_in(y, x),
  which_in(y, x),
  which_in2(y, x),
  which(y %in% x)
)
*/

Calling sourceCpp on this gives me, from the benchmark,

Unit: microseconds
            expr    min      lq  median      uq    max neval
  sugar_in(y, x)  7.590 10.0795 11.4825 14.3630 32.753   100
  which_in(y, x) 40.757 42.4460 43.4400 46.8240 63.690   100
 which_in2(y, x) 14.325 15.2365 16.7005 17.2620 30.580   100
 which(y %in% x) 17.070 21.6145 23.7070 29.0105 78.009   100

回答2:

For this set of inputs we can eke out a little more performance by using an approach that technically has a higher algorithmic complexity (O(ln n) vs O(1) for each lookup) but has lower constants: a binary search.

// [[Rcpp::plugins("cpp11")]]
#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
std::vector<int> which_in(IntegerVector x, IntegerVector y) {
  int nx = x.size();
  std::unordered_set<int> z(y.begin(), y.end());
  std::vector<int> output;
  output.reserve(nx);
  for (int i=0; i < nx; ++i) {
    if (z.find( x[i] ) != z.end() ) {
      output.push_back(i+1);
    }
  }
  return output;
}

// [[Rcpp::export]]
std::vector<int> which_in2(IntegerVector x, IntegerVector y) {
  std::vector<int> y_sort(y.size());
  std::partial_sort_copy (y.begin(), y.end(), y_sort.begin(), y_sort.end());

  int nx = x.size();
  std::vector<int> out;

  for (int i = 0; i < nx; ++i) {
    std::vector<int>::iterator found =
      lower_bound(y_sort.begin(), y_sort.end(), x[i]);
    if (found != y_sort.end()) {
      out.push_back(i + 1);
    }
  }
  return out;
}

/*** R
set.seed(123)
library(microbenchmark)
x <- sample(1:100)
y <- sample(1:10000, 1000)
identical( which_in(y, x), which(y %in% x) )
identical( which_in2(y, x), which(y %in% x) )
microbenchmark(
  which_in(y, x),
  which_in2(y, x),
  which(y %in% x)
)
*/

On my computer that yields

Unit: microseconds
            expr  min   lq median   uq  max neval
  which_in(y, x) 39.3 41.0   42.7 44.0 81.5   100
 which_in2(y, x) 12.8 13.6   14.4 15.0 23.8   100
 which(y %in% x) 16.8 20.2   21.0 21.9 31.1   100

so about 30% better than base R.

来源：https://stackoverflow.com/questions/21359432/a-c-version-of-the-in-operator-in-r

标签

c++

rcpp

armadillo